Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: SERBP1

Gene summary for SERBP1

Gene summary.

Gene information	Species	Human
	Gene symbol	SERBP1
	Gene ID	26135
	Gene name	SERPINE1 mRNA binding protein 1
	Gene Alias	CGI-55
	Cytomap	1p31.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q8NC51

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
26135	SERBP1	CA_HPV_1	Human	Cervix	CC	1.81e-06	-6.72e-02	0.0264
26135	SERBP1	CA_HPV_3	Human	Cervix	CC	1.80e-03	1.39e-01	0.0414
26135	SERBP1	N_HPV_2	Human	Cervix	N_HPV	1.29e-02	1.18e-01	-0.0131
26135	SERBP1	CCII_1	Human	Cervix	CC	4.19e-29	-9.19e-01	0.3249
26135	SERBP1	sample1	Human	Cervix	CC	4.52e-06	-4.62e-01	0.0959
26135	SERBP1	sample3	Human	Cervix	CC	5.59e-05	-2.17e-02	0.1387
26135	SERBP1	L1	Human	Cervix	CC	2.57e-07	-6.48e-02	0.0802
26135	SERBP1	T1	Human	Cervix	CC	7.57e-20	-5.51e-01	0.0918
26135	SERBP1	T3	Human	Cervix	CC	1.03e-03	-1.22e-02	0.1389
26135	SERBP1	HTA11_1938_2000001011	Human	Colorectum	AD	1.90e-07	6.91e-01	-0.0811
26135	SERBP1	HTA11_78_2000001011	Human	Colorectum	AD	2.61e-08	6.90e-01	-0.1088
26135	SERBP1	HTA11_347_2000001011	Human	Colorectum	AD	5.40e-22	9.97e-01	-0.1954
26135	SERBP1	HTA11_83_2000001011	Human	Colorectum	SER	2.40e-04	6.10e-01	-0.1526
26135	SERBP1	HTA11_696_2000001011	Human	Colorectum	AD	1.35e-10	6.40e-01	-0.1464
26135	SERBP1	HTA11_866_2000001011	Human	Colorectum	AD	1.04e-05	4.79e-01	-0.1001
26135	SERBP1	HTA11_1391_2000001011	Human	Colorectum	AD	3.08e-12	9.71e-01	-0.059
26135	SERBP1	HTA11_546_2000001011	Human	Colorectum	AD	3.15e-04	5.89e-01	-0.0842
26135	SERBP1	HTA11_866_3004761011	Human	Colorectum	AD	3.49e-09	6.62e-01	0.096
26135	SERBP1	HTA11_7663_2000001011	Human	Colorectum	SER	1.19e-05	8.94e-01	0.0131
26135	SERBP1	HTA11_10623_2000001011	Human	Colorectum	AD	6.85e-03	6.59e-01	-0.0177

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:00064029	Cervix	CC	mRNA catabolic process	56/2311	232/18723	4.81e-07	1.83e-05	56
GO:19033119	Cervix	CC	regulation of mRNA metabolic process	64/2311	288/18723	1.71e-06	5.64e-05	64
GO:00064019	Cervix	CC	RNA catabolic process	62/2311	278/18723	2.18e-06	6.56e-05	62
GO:00610139	Cervix	CC	regulation of mRNA catabolic process	38/2311	166/18723	1.07e-04	1.36e-03	38
GO:00467008	Cervix	CC	heterocycle catabolic process	80/2311	445/18723	3.23e-04	3.42e-03	80
GO:00346559	Cervix	CC	nucleobase-containing compound catabolic process	74/2311	407/18723	3.77e-04	3.88e-03	74
GO:00434889	Cervix	CC	regulation of mRNA stability	35/2311	158/18723	3.80e-04	3.89e-03	35
GO:00434879	Cervix	CC	regulation of RNA stability	36/2311	170/18723	7.72e-04	6.86e-03	36
GO:00442709	Cervix	CC	cellular nitrogen compound catabolic process	79/2311	451/18723	7.80e-04	6.91e-03	79
GO:00194398	Cervix	CC	aromatic compound catabolic process	79/2311	467/18723	2.14e-03	1.54e-02	79
GO:19013618	Cervix	CC	organic cyclic compound catabolic process	80/2311	495/18723	6.77e-03	3.72e-02	80
GO:000640214	Cervix	N_HPV	mRNA catabolic process	17/534	232/18723	3.76e-04	5.43e-03	17
GO:190331114	Cervix	N_HPV	regulation of mRNA metabolic process	18/534	288/18723	1.63e-03	1.68e-02	18
GO:000640114	Cervix	N_HPV	RNA catabolic process	17/534	278/18723	2.72e-03	2.39e-02	17
GO:1903311	Colorectum	AD	regulation of mRNA metabolic process	117/3918	288/18723	1.69e-14	4.23e-12	117
GO:0006401	Colorectum	AD	RNA catabolic process	102/3918	278/18723	8.64e-10	6.76e-08	102
GO:0044270	Colorectum	AD	cellular nitrogen compound catabolic process	147/3918	451/18723	3.35e-09	2.23e-07	147
GO:0046700	Colorectum	AD	heterocycle catabolic process	145/3918	445/18723	4.37e-09	2.84e-07	145
GO:0006402	Colorectum	AD	mRNA catabolic process	87/3918	232/18723	4.40e-09	2.84e-07	87
GO:0034655	Colorectum	AD	nucleobase-containing compound catabolic process	133/3918	407/18723	1.56e-08	9.12e-07	133

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

SERBP1

SNV

Missense_Mutation

novel

c.197N>A

p.Ala66Glu

p.A66E

Q8NC51

protein_coding

deleterious(0.03)

probably_damaging(0.987)

TCGA-AR-A1AL-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

anastrozole

SERBP1

SNV

Missense_Mutation

c.448G>A

p.Glu150Lys

p.E150K

Q8NC51

protein_coding

tolerated(0.21)

probably_damaging(0.988)

TCGA-D8-A27N-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxol+adriamycin+cyclophosphamide+herceptin

SERBP1

SNV

Missense_Mutation

novel

c.845N>T

p.Glu282Val

p.E282V

Q8NC51

protein_coding

deleterious(0)

probably_damaging(0.917)

TCGA-E2-A15S-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SERBP1

SNV

Missense_Mutation

rs767934992

c.562C>T

p.Arg188Cys

p.R188C

Q8NC51

protein_coding

deleterious(0)

possibly_damaging(0.796)

TCGA-IR-A3LF-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SERBP1

SNV

Missense_Mutation

c.946G>A

p.Asp316Asn

p.D316N

Q8NC51

protein_coding

tolerated(0.34)

benign(0.145)

TCGA-JX-A5QV-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SERBP1

SNV

Missense_Mutation

novel

c.901N>T

p.Arg301Trp

p.R301W

Q8NC51

protein_coding

tolerated(0.06)

benign(0.178)

TCGA-VS-A9UH-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SERBP1

insertion

Nonsense_Mutation

novel

c.567_568insTCCAAATGCTTATTCATAACATTTTTATGTAATCTTAATAGGTAAG

p.Lys190SerfsTer15

p.K190Sfs*15

Q8NC51

protein_coding

TCGA-EA-A5O9-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SERBP1

SNV

Missense_Mutation

novel

c.1055N>T

p.Thr352Met

p.T352M

Q8NC51

protein_coding

tolerated(0.05)

benign(0.36)

TCGA-A6-2672-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

SERBP1

SNV

Missense_Mutation

c.295N>A

p.Val99Met

p.V99M

Q8NC51

protein_coding

tolerated(0.16)

possibly_damaging(0.682)

TCGA-AA-A00O-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

SERBP1

SNV

Missense_Mutation

novel

c.892N>G

p.Asn298Asp

p.N298D

Q8NC51

protein_coding

tolerated(0.83)

benign(0.006)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID

Symbol

Category

Interaction Types

Drug Claim Name

Drug Name

PMIDs

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